Notes on installing and using the PyNAST command line application.
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PyNAST is a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rRNA sequences to existing 16s rRNA alignments. This reimplementation is more flexible, faster, and easier to install and maintain than the original NAST implementation. PyNAST is built using the PyCogent Bioinformatics Toolkit (PyCogent).
The first versions of PyNAST (through PyNAST 1.0) were written to exactly match the results of the original NAST algorithm. Beginning with the post-PyNAST 1.0 development code, PyNAST no longer exactly matches the NAST output but is instead focused on getting better alignments. Users who wish to exactly match the results of NAST should download PyNAST 1.0.
Given a set of sequences and a template alignment, PyNAST will align the input sequences against the template alignment, and return a multiple sequence alignment which contains the same number of positions (or columns) as the template alignment. This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rRNA sequences.
PyNAST is presented in an open access Bioinformatics Applications Note.
PyNAST is distributed under the terms of the Modified BSD License. The full license is in the file COPYING.txt, distributed with this software.
If you make use of PyNAST in published work, please cite:
PyNAST: a flexible tool for aligning sequences to a template alignment. J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight. January 15, 2010, DOI 10.1093/bioinformatics/btp636. Bioinformatics 26: 266-267.
Requests for help with PyNAST should be directed to the QIIME Forum.